A sample of key scientific discoveries about the bugs inside you

By Sabin Russell | Illustration by Breanna Welsh

THE HUMAN MICROBIOME had been largely uncharted until the last decade, when high-speed gene sequencing machines cracked it open for study and researchers began pouring into the field. In the past few years alone, the number of studies published in academic journals on microbiome research has soared. To highlight the breadth and excitement of new discoveries about the human microbiome, here is a snapshot of just five recent surprising and important findings that may affect your health.

When a once-promising HIV vaccine failed completely in a global trial three years ago, scientists wanted to know why. Last year came a revelation: It may have been interference from common bacteria in the human gut. Duke Medicine researchers, with help from Fred Hutch scientists, found the candidate vaccine essentially stirred up the wrong antibodies — showing for the first time that gut bacteria can modify an immune response to a vaccine.

Antibodies are proteins that our immune system generates to target features on the surface of invading microbes. But instead of producing new antibodies against HIV, this experimental vaccine awakened old antibodies formed against gut bacteria acquired during early childhood.

Dr. Jim Kublin of Fred Hutch's Vaccine and Infectious Disease Division helped oversee the HIV vaccine trial, and this fall was awarded a five-year, $4 million grant from the National Institute of Allergy and Infectious Diseases to study exactly how gut microbes can alter immune responses. The study could not only lead to a better HIV vaccine, it could show how the immune response to gut bacteria might be tapped to build more effective vaccines of all kinds.

A pair of mouse studies, conducted continents apart, has shown that specific kinds of gut bacteria can directly affect the immune system’s response against cancer. A University of Chicago study found that mice with the common gut bacterium Bifidobacterium had better anti-tumor activity against melanoma than mice without it.

Significantly, an immunotherapy drug known as a checkpoint inhibitor — the same treatment credited with saving former President Jimmy Carter’s life — worked better in the mice with Bifidobacterium. A French study of a different checkpoint inhibitor found that the drug failed against melanoma in “germ free” mice, but the anti-cancer properties of the drug were restored when the mice were fed Bacteroides fragilis.

Checkpoint inhibitor therapy works for some patients, not for others. Both studies suggest that changes in a patient’s microbiome might improve the efficacy of immunotherapy.

A study by the Providence Saint John’s Health Center in Santa Monica, California, found that women with a history of breast cancer had a distinctly different community of microbes in their breast ducts compared to healthy controls. Until recently, it was assumed that breast tissue, nipple aspirate fluid and milk were sterile. Studies are underway to find out if the bacteria found in breast fluid could promote or inhibit DNA damage that can turn cells cancerous.

Disruptions to the balance of microbial species in the human gut have been associated with several gastrointestinal diseases, including inflammatory bowel disease, irritable bowel syndrome, nonalcoholic fatty liver disease and bowel cancers.

A study of Finnish children at risk for diabetes showed they were more likely than their Russian counterparts to develop the autoimmune disease. One possibility: It’s in the water. The Russian children grew up drinking from a less sanitary source of water and have a different community of gut bugs that may better calibrate their immune cells to distinguish foreign microbes from their own tissues.

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